vcf2diploid

vcf2diploid constructs a diploid personal genome by integrating individual variants to enable allele-specific expression (ASE) and allele-specific binding (ASB) analyses.

Key Features:

• Personalized Genome Construction: Constructs a diploid personal genome sequence by integrating SNPs, insertions/deletions (indels), and structural variants into a reference genome.
• Gene Annotation: Generates corresponding personalized gene annotations for the constructed diploid genome.
• Bias Mitigation in Read Mapping: Addresses read mapping bias toward reference alleles to improve allele-specific signal detection.
• ASE and ASB Identification: Compares mapped reads between maternal and paternal alleles to identify allele-specific expression and binding events.

Scientific Applications:

• Functional Genomic Studies: Applied to NA12878 data from the 1000 Genomes Project with matched RNA-Seq and ChIP-Seq datasets to observe allele-specific behaviors.
• X-Chromosome Inactivation Analysis: Enables analysis of allele-specific patterns relevant to X-chromosome inactivation.
• Regulatory Network Framework: Facilitates investigation of interactions between ASE and ASB across multiple transcription factor events.
• Correlation and Network Motifs Analysis: Supports correlation analyses and examination of network motifs to reveal coordination between ASB and ASE.

Methodology:

Incorporates SNPs, indels, and structural variants into a reference genome to construct a personalized diploid genome; aligns sequencing reads to the personal genome while correcting mapping bias toward reference alleles; identifies significant differences in read counts between maternal and paternal alleles to detect ASE and ASB.